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DNA polymerase III holoenzyme is the primary
enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products ...
complex involved in
prokaryotic A prokaryote () is a single-celled organism that lacks a nucleus and other membrane-bound organelles. The word ''prokaryote'' comes from the Greek πρό (, 'before') and κάρυον (, 'nut' or 'kernel').Campbell, N. "Biology:Concepts & Connec ...
DNA replication In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...
. It was discovered by Thomas Kornberg (son of
Arthur Kornberg Arthur Kornberg (March 3, 1918 – October 26, 2007) was an American biochemist who won the Nobel Prize in Physiology or Medicine 1959 for the discovery of "the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic ac ...
) and Malcolm Gefter in 1970. The complex has high processivity (i.e. the number of
nucleotide Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monomeric units of the nucleic acid polymers – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecule ...
s added per binding event) and, specifically referring to the replication of the '' E.coli''
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding g ...
, works in conjunction with four other DNA polymerases (
Pol I DNA polymerase I (or Pol I) is an enzyme that participates in the process of prokaryotic DNA replication. Discovered by Arthur Kornberg in 1956, it was the first known DNA polymerase (and the first known of any kind of polymerase). It was initia ...
, Pol II, Pol IV, and
Pol V DNA Polymerase V (Pol V) is a polymerase enzyme involved in DNA repair mechanisms in bacteria, such as ''Escherichia coli''. It is composed of a UmuD' homodimer and a UmuC monomer, forming the UmuD'2C protein complex. It is part of the Y-family o ...
). Being the primary
holoenzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. ...
involved in replication activity, the DNA Pol III
holoenzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. ...
also has proofreading capabilities that corrects replication mistakes by means of exonuclease activity reading 3'→5' and synthesizing 5'→3'. DNA Pol III is a component of the
replisome The replisome is a complex molecular machine that carries out replication of DNA. The replisome first unwinds double stranded DNA into two single strands. For each of the resulting single strands, a new complementary sequence of DNA is synt ...
, which is located at the replication fork.


Components

The replisome is composed of the following: *2 DNA Pol III enzymes, each comprising α, ε and θ subunits. (It has been proven that there is a third copy of Pol III at the replisome.) **the α subunit (encoded by the
dnaE DnaE, the gene product of ''dnaE'', is the catalytic α subunit of DNA polymerase III, acting as a DNA polymerase. This enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules u ...
gene) has the polymerase activity. **the ε subunit (
dnaQ ''dnaQ'' is the gene encoding the ε subunit of DNA polymerase III in ''Escherichia coli''. The ε subunit is one of three core proteins in the DNA polymerase complex. It functions as a 3’→5’ DNA directed proofreading exonuclease that rem ...
) has 3'→5' exonuclease activity. **the θ subunit (
holE A hole is an opening in or through a particular medium, usually a solid body. Holes occur through natural and artificial processes, and may be useful for various purposes, or may represent a problem needing to be addressed in many fields of en ...
) stimulates the ε subunit's proofreading. *2 β units ( dnaN) which act as sliding
DNA clamp A DNA clamp, also known as a sliding clamp, is a protein complex that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevent ...
s, they keep the polymerase bound to the DNA. *2 τ units (
dnaX The τ and γ subunits are part of the DNA polymerase III holoenzyme DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Kornberg (son of Arthur Kornberg) and Malc ...
) which act to dimerize two of the core enzymes (α, ε, and θ subunits). *1 γ unit (also dnaX) which acts as a clamp loader for the lagging strand
Okazaki fragment Okazaki fragments are short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA ...
s, helping the two β subunits to form a unit and bind to DNA. The γ unit is made up of 5 γ subunits which include 3 γ subunits, 1 δ subunit (
holA In molecular biology, the δ (delta) subunit of DNA polymerase III is encoded by the holA gene in '' E. coli'' and other bacteria Bacteria (; singular: bacterium) are ubiquitous, mostly free-living organisms often consisting of one bio ...
), and 1 δ' subunit (
holB In '' E. coli'' and other bacteria, holB is a gene that encodes the delta prime subunit of DNA polymerase III DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas Korn ...
). The δ is involved in copying of the lagging strand. * Χ (
holC In '' E. coli'' and other bacteria, holC is a gene that encodes the chi subunit of DNA polymerase III DNA polymerase III holoenzyme is the primary enzyme complex involved in prokaryotic DNA replication. It was discovered by Thomas B. Kornberg, ...
) and Ψ (
holD Hold may refer to: Physical spaces * Hold (ship), interior cargo space * Baggage hold, cargo space on an airplane * Stronghold, a castle or other fortified place Arts, entertainment, and media * Hold (musical term), a pause, also called a Ferm ...
) which form a 1:1 complex and bind to γ or τ. X can also mediate the switch from RNA primer to DNA.


Activity

DNA polymerase III synthesizes base pairs at a rate of around 1000 nucleotides per second. DNA Pol III activity begins after strand separation at the origin of replication. Because DNA synthesis cannot start ''de novo'', an RNA primer, complementary to part of the single-stranded DNA, is synthesized by
primase DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA (or DNA in some living organisms) segment called a primer complementary to a ssDNA (single-stranded ...
(an RNA polymerase): ("!" for RNA, '"$" for DNA, "*" for polymerase) --------> * * * * ! ! ! ! _ _ _ _ _ _ _ _ , RNA , <--
ribose Ribose is a simple sugar and carbohydrate with molecular formula C5H10O5 and the linear-form composition H−(C=O)−(CHOH)4−H. The naturally-occurring form, , is a component of the ribonucleotides from which RNA is built, and so this compo ...
(sugar)-phosphate backbone G U A U , Pol , <-- RNA primer * * * * , _ _ _ _, <--hydrogen bonding C A T A G C A T C C <--
template Template may refer to: Tools * Die (manufacturing), used to cut or shape material * Mold, in a molding process * Stencil, a pattern or overlay used in graphic arts (drawing, painting, etc.) and sewing to replicate letters, shapes or designs ...
ss DNA (single-stranded DNA) _ _ _ _ _ _ _ _ _ _ <--
deoxyribose Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone $ $ $ $ $ $ $ $ $ $


Addition onto 3'OH

As replication progresses and the
replisome The replisome is a complex molecular machine that carries out replication of DNA. The replisome first unwinds double stranded DNA into two single strands. For each of the resulting single strands, a new complementary sequence of DNA is synt ...
moves forward, DNA polymerase III arrives at the RNA primer and begins replicating the DNA, adding onto the 3'OH of the primer: * * * * ! ! ! ! _ _ _ _ _ _ _ _ , DNA , <--
deoxyribose Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone G U A U , Pol , <-- RNA primer * * * * , _III_ _, <--hydrogen bonding C A T A G C A T C C <--
template Template may refer to: Tools * Die (manufacturing), used to cut or shape material * Mold, in a molding process * Stencil, a pattern or overlay used in graphic arts (drawing, painting, etc.) and sewing to replicate letters, shapes or designs ...
ss DNA (single-stranded DNA) _ _ _ _ _ _ _ _ _ _ <--
deoxyribose Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone $ $ $ $ $ $ $ $ $ $


Synthesis of DNA

DNA polymerase III will then synthesize a continuous or discontinuous strand of DNA, depending if this is occurring on the leading or lagging strand (
Okazaki fragment Okazaki fragments are short sequences of DNA nucleotides (approximately 150 to 200 base pairs long in eukaryotes) which are synthesized discontinuously and later linked together by the enzyme DNA ligase to create the lagging strand during DNA ...
) of the DNA. DNA polymerase III has a high processivity and therefore, synthesizes DNA very quickly. This high processivity is due in part to the β-clamps that "hold" onto the DNA strands. -----------> * * * * ! ! ! ! $ $ $ $ $ $ _ _ _ _ _ _ _ _ _ _ _ _ _ _, DNA , <--
deoxyribose Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone G U A U C G T A G G, Pol , <-- RNA primer * * * * * * * * * *, _III_ _, <--hydrogen bonding C A T A G C A T C C <--
template Template may refer to: Tools * Die (manufacturing), used to cut or shape material * Mold, in a molding process * Stencil, a pattern or overlay used in graphic arts (drawing, painting, etc.) and sewing to replicate letters, shapes or designs ...
ss DNA (single-stranded DNA) _ _ _ _ _ _ _ _ _ _ <--
deoxyribose Deoxyribose, or more precisely 2-deoxyribose, is a monosaccharide with idealized formula H−(C=O)−(CH2)−(CHOH)3−H. Its name indicates that it is a deoxy sugar, meaning that it is derived from the sugar ribose by loss of a hydroxy group. D ...
(sugar)-phosphate backbone $ $ $ $ $ $ $ $ $ $


Removal of primer

After replication of the desired region, the RNA primer is removed by
DNA polymerase I DNA polymerase I (or Pol I) is an enzyme that participates in the process of prokaryotic DNA replication. Discovered by Arthur Kornberg in 1956, it was the first known DNA polymerase (and the first known of any kind of polymerase). It was initi ...
via the process of
nick translation Nick translation (or head translation), developed in 1977 by Peter Rigby and Paul Berg, is a tagging technique in molecular biology in which DNA Polymerase I is used to replace some of the nucleotides of a DNA sequence with their labeled analogu ...
. The removal of the RNA primer allows
DNA ligase DNA ligase is a specific type of enzyme, a ligase, () that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living orga ...
to ligate the DNA-DNA nick between the new fragment and the previous strand. DNA polymerase I & III, along with many other enzymes are all required for the high fidelity, high-processivity of DNA replication.


See also

* Beta clamp *
DNA polymerase A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create ...
*
DNA replication In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part for biological inheritanc ...


References


External links


Overview
at
Oregon State University Oregon State University (OSU) is a public land-grant, research university in Corvallis, Oregon. OSU offers more than 200 undergraduate-degree programs along with a variety of graduate and doctoral degrees. It has the 10th largest engineering c ...
*
Clamping down on pathogenic bacteria
– how to shut down a key DNA polymerase complex {{Portal bar, Biology, border=no EC 2.7.7 DNA replication Enzymes Protein complexes